PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of outdoor ranging on external and internal health parameters for hens from different rearing enrichments
items: Albumin promotes proliferation of G1 arrested serum starved hepatocellular carcinoma cells
items: Temporal predictability does not impact attentional blink performance: effects of fixed vs. random inter-trial intervals
items: Molecular docking and network connections of active compounds from the classical herbal formula Ding Chuan Tang
items: Diversity of fall armyworm, Spodoptera frugiperda and their gut bacterial community in Kenya
items: Application of a high-quality, high-volume trap–neuter–return model of community cats in Seoul, Korea
items: Congenital feeding response to a novel prey in a Mexican gartersnake
items: Genome-wide investigation of WRKY transcription factors in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating growth and development
items: Common and specific gene signatures among three different endometriosis subtypes
items: Characterisation of GLUT4 trafficking in HeLa cells: comparable kinetics and orthologous trafficking mechanisms to 3T3-L1 adipocytes

Effects of outdoor ranging on external and internal health parameters for hens from different rearing enrichments
type: item
type: AcademicArticle
description: In Australia, free-range layer pullets are typically reared indoors, but adult layers go outdoors, and this mismatch might reduce adaptation in laying environments. Enrichments during rearing may optimise pullet development and subsequent welfare as adult free-range hens. In the outdoor environment, hens may have greater opportunities for exercise and natural behaviours which might contribute to improved health and welfare. However, the outdoor environment may also result in potential exposure to parasites and pathogens. Individual variation in range use may thus dictate individual health and welfare. This study was conducted to evaluate whether adult hens varied in their external and internal health due to rearing enrichments and following variation in range use. A total of 1386 Hy-Line Brown® chicks were reared indoors across 16 weeks with three enrichment treatments including a control group with standard housing conditions, a novelty group providing novel objects that changed weekly, and a structural group with custom-designed structures to increase spatial navigation and perching. At 16 weeks of age the pullets were moved to a free-range system and housed in nine identical pens within their rearing treatments. All hens were leg-banded with microchips and daily ranging was assessed from 25 to 64 weeks via radio-frequency identification technology. At 64–65 weeks of age, 307 hens were selected based on their range use patterns across 54 days up to 64 weeks: indoor (no ranging), low outdoor (1.4 h or less daily), and high outdoor (5.2–9 h daily). The external and internal health and welfare parameters were evaluated via external assessment of body weight, plumage, toenails, pecking wounds, illness, and post-mortem assessment of internal organs and keel bones including whole-body CT scanning for body composition. The control hens had the lowest feather coverage (p < 0.0001) and a higher number of comb wounds (P = 0.03) than the novelty hens. The high outdoor ranger…
format: application/pdf
format: text/html
creator: Md Saiful Bari
creator: Yan C.S.M. Laurenson
creator: Andrew M. Cohen-Barnhouse
creator: Stephen W. Walkden-Brown
creator: Dana L.M. Campbell
subject: Agricultural Science
subject: Animal Behavior
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.8720
publisher: PeerJ Inc.
rights: © 2020 Bari et al.
abstract: In Australia, free-range layer pullets are typically reared indoors, but adult layers go outdoors, and this mismatch might reduce adaptation in laying environments. Enrichments during rearing may optimise pullet development and subsequent welfare as adult free-range hens. In the outdoor environment, hens may have greater opportunities for exercise and natural behaviours which might contribute to improved health and welfare. However, the outdoor environment may also result in potential exposure to parasites and pathogens. Individual variation in range use may thus dictate individual health and welfare. This study was conducted to evaluate whether adult hens varied in their external and internal health due to rearing enrichments and following variation in range use. A total of 1386 Hy-Line Brown® chicks were reared indoors across 16 weeks with three enrichment treatments including a control group with standard housing conditions, a novelty group providing novel objects that changed weekly, and a structural group with custom-designed structures to increase spatial navigation and perching. At 16 weeks of age the pullets were moved to a free-range system and housed in nine identical pens within their rearing treatments. All hens were leg-banded with microchips and daily ranging was assessed from 25 to 64 weeks via radio-frequency identification technology. At 64–65 weeks of age, 307 hens were selected based on their range use patterns across 54 days up to 64 weeks: indoor (no ranging), low outdoor (1.4 h or less daily), and high outdoor (5.2–9 h daily). The external and internal health and welfare parameters were evaluated via external assessment of body weight, plumage, toenails, pecking wounds, illness, and post-mortem assessment of internal organs and keel bones including whole-body CT scanning for body composition. The control hens had the lowest feather coverage (p < 0.0001) and a higher number of comb wounds (P = 0.03) than the novelty hens. The high outdoor ranger…
bibliographic citation: Bari et al. (2020) Effects of outdoor ranging on external and internal health parameters for hens from different rearing enrichments. PeerJ 8:e8720 https://doi.org/10.7717/peerj.8720
date submitted: 2019-11-19
date accepted: 2020-02-10
issued: 2020-03-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bari
  given name: Md Saiful
author list: Agent
  family name: Laurenson
  given name: Yan C.S.M.
author list: Agent
  family name: Cohen-Barnhouse
  given name: Andrew M.
author list: Agent
  family name: Walkden-Brown
  given name: Stephen W.
author list: Agent
  family name: Campbell
  given name: Dana L.M.
doi: 10.7717/peerj.8720
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-06
copyright: ©2020 Bari et al.
attribution name: Bari et al.

Albumin promotes proliferation of G1 arrested serum starved hepatocellular carcinoma cells
type: item
type: AcademicArticle
description: Albumin is the most abundant plasma protein and functions as a transport molecule that continuously interacts with various cell types. Because of these properties, albumin has been exploited by the pharmaceutical industry to improve drug delivery into target cells. The immediate effects of albumin on cells, however, require further understanding. The cell interacting properties and pharmaceutical applications of albumin incentivises continual research into the immediate effects of albumin on cells. The HepG2/C3A hepatocellular carcinoma cell line is used as a model for studying cancer pathology as well as liver biosynthesis and cellular responses to drugs. Here we investigated the direct effect of purified albumin on HepG2/C3A cell proliferation in the absence of serum, growth factors and other serum originating albumin bound molecules. We observed that the reduced cell counts in serum starved HepG2/C3A cultures were increased by the inclusion of albumin. Cell cycle analysis demonstrated that the percentage of cells in G1 phase during serum starvation was reduced from 86.4 ± 2.3% to 78.3 ± 3.2% by the inclusion of albumin whereas the percentage of cells in S phase was increased from 6.5 ± 1.5% to 14.3 ± 3.6%. A significant reduction in the cell cycle inhibitor protein, P21, accompanied the changes in the proportions of cell cycle phases upon treatment with albumin. We have also observed that the levels of dead cells determined by DNA fragmentation and membrane permeabilization caused by serum starvation (TUNEL: 16.6 ± 7.2%, ethidium bromide: 13.8 ± 4.8%) were not significantly altered by the inclusion of albumin (11.6 ± 10.2%, ethidium bromide: 16.9 ± 8.9%). Therefore, the increase in cell number was mainly caused by albumin promoting proliferation rather than protection against cell death. These primary findings demonstrate that albumin has immediate effects on HepG2/C3A hepatocellular carcinoma cells. These effects should be taken into consideration when studying …
format: application/pdf
format: text/html
creator: Badr Ibrahim
creator: Jan Stange
creator: Adrian Dominik
creator: Martin Sauer
creator: Sandra Doss
creator: Martin Eggert
subject: Biochemistry
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.8568
publisher: PeerJ Inc.
rights: © 2020 Ibrahim et al.
abstract: Albumin is the most abundant plasma protein and functions as a transport molecule that continuously interacts with various cell types. Because of these properties, albumin has been exploited by the pharmaceutical industry to improve drug delivery into target cells. The immediate effects of albumin on cells, however, require further understanding. The cell interacting properties and pharmaceutical applications of albumin incentivises continual research into the immediate effects of albumin on cells. The HepG2/C3A hepatocellular carcinoma cell line is used as a model for studying cancer pathology as well as liver biosynthesis and cellular responses to drugs. Here we investigated the direct effect of purified albumin on HepG2/C3A cell proliferation in the absence of serum, growth factors and other serum originating albumin bound molecules. We observed that the reduced cell counts in serum starved HepG2/C3A cultures were increased by the inclusion of albumin. Cell cycle analysis demonstrated that the percentage of cells in G1 phase during serum starvation was reduced from 86.4 ± 2.3% to 78.3 ± 3.2% by the inclusion of albumin whereas the percentage of cells in S phase was increased from 6.5 ± 1.5% to 14.3 ± 3.6%. A significant reduction in the cell cycle inhibitor protein, P21, accompanied the changes in the proportions of cell cycle phases upon treatment with albumin. We have also observed that the levels of dead cells determined by DNA fragmentation and membrane permeabilization caused by serum starvation (TUNEL: 16.6 ± 7.2%, ethidium bromide: 13.8 ± 4.8%) were not significantly altered by the inclusion of albumin (11.6 ± 10.2%, ethidium bromide: 16.9 ± 8.9%). Therefore, the increase in cell number was mainly caused by albumin promoting proliferation rather than protection against cell death. These primary findings demonstrate that albumin has immediate effects on HepG2/C3A hepatocellular carcinoma cells. These effects should be taken into consideration when studying …
bibliographic citation: Ibrahim et al. (2020) Albumin promotes proliferation of G1 arrested serum starved hepatocellular carcinoma cells. PeerJ 8:e8568 https://doi.org/10.7717/peerj.8568
date submitted: 2019-05-13
date accepted: 2020-01-15
issued: 2020-03-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ibrahim
  given name: Badr
author list: Agent
  family name: Stange
  given name: Jan
author list: Agent
  family name: Dominik
  given name: Adrian
author list: Agent
  family name: Sauer
  given name: Martin
author list: Agent
  family name: Doss
  given name: Sandra
author list: Agent
  family name: Eggert
  given name: Martin
doi: 10.7717/peerj.8568
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-05
copyright: ©2020 Ibrahim et al.
attribution name: Ibrahim et al.

Temporal predictability does not impact attentional blink performance: effects of fixed vs. random inter-trial intervals
type: item
type: AcademicArticle
description: Background Does the inclusion of a randomized inter-trial interval (ITI) impact performance on an Attentional Blink (AB) task? The AB phenomenon is often used as a test of transient attention (Dux & Marois, 2009); however, it is unclear whether incorporating aspects of sustained attention, by implementing a randomized ITI, would impact task performance. The current research sought to investigate this, by contrasting a standard version of the AB task with a random ITI version to determine whether performance changed, reflecting a change in difficulty, engagement, or motivation. Method Thirty university students (21 female; age range 18–57, Mage= 21.5, SD = 7.4) completed both versions of the task, in counterbalanced order. Results No significant difference in performance was found between the standard AB task and the AB task with the random ITI. Bayesian analyses suggested moderate evidence for the null. Conclusion Temporal unpredictability did not appear to impact task performance. This suggests that the standard AB task has cognitive properties with regards to task difficulty, engagement, and motivation, that are inherently similar to tasks that employ a randomized ITI to measure sustained attention (e.g., the Psychomotor Vigilance Task; PVT; Dinges & Powell, 1985). This finding provides important support for future research which may seek to obtain a more detailed understanding of attention through the comparison of performance on transient and sustained attention tasks.
format: application/pdf
format: text/html
creator: Lucienne Shenfield
creator: Vanessa Beanland
creator: Deborah Apthorp
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8677
publisher: PeerJ Inc.
rights: © 2020 Shenfield et al.
abstract: Background Does the inclusion of a randomized inter-trial interval (ITI) impact performance on an Attentional Blink (AB) task? The AB phenomenon is often used as a test of transient attention (Dux & Marois, 2009); however, it is unclear whether incorporating aspects of sustained attention, by implementing a randomized ITI, would impact task performance. The current research sought to investigate this, by contrasting a standard version of the AB task with a random ITI version to determine whether performance changed, reflecting a change in difficulty, engagement, or motivation. Method Thirty university students (21 female; age range 18–57, Mage= 21.5, SD = 7.4) completed both versions of the task, in counterbalanced order. Results No significant difference in performance was found between the standard AB task and the AB task with the random ITI. Bayesian analyses suggested moderate evidence for the null. Conclusion Temporal unpredictability did not appear to impact task performance. This suggests that the standard AB task has cognitive properties with regards to task difficulty, engagement, and motivation, that are inherently similar to tasks that employ a randomized ITI to measure sustained attention (e.g., the Psychomotor Vigilance Task; PVT; Dinges & Powell, 1985). This finding provides important support for future research which may seek to obtain a more detailed understanding of attention through the comparison of performance on transient and sustained attention tasks.
bibliographic citation: Shenfield et al. (2020) Temporal predictability does not impact attentional blink performance: effects of fixed vs. random inter-trial intervals. PeerJ 8:e8677 https://doi.org/10.7717/peerj.8677
date submitted: 2019-10-21
date accepted: 2020-02-03
issued: 2020-03-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shenfield
  given name: Lucienne
author list: Agent
  family name: Beanland
  given name: Vanessa
author list: Agent
  family name: Apthorp
  given name: Deborah
doi: 10.7717/peerj.8677
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-05
copyright: ©2020 Shenfield et al.
attribution name: Shenfield et al.

Molecular docking and network connections of active compounds from the classical herbal formula Ding Chuan Tang
type: item
type: AcademicArticle
description: Background Ding Chuan Tang (DCT), a traditional Chinese herbal formula, has been consistently prescribed for the therapeutic management of wheezing and asthma-related indications since the Song Dynasty (960–1279 AD). This study aimed to identify molecular network pharmacology connections to understand the biological asthma-linked mechanisms of action of DCT and potentially identify novel avenues for asthma drug development. Methods Employing molecular docking (AutoDock Vina) and computational analysis (Cytoscape 3.6.0) strategies for DCT compounds permitted examination of docking connections for proteins that were targets of DCT compounds and asthma genes. These identified protein targets were further analyzed to establish and interpret network connections associated with asthma disease pathways. Results A total of 396 DCT compounds and 234 asthma genes were identified through database search. Computational molecular docking of DCT compounds identified five proteins (ESR1, KDR, LTA4H, PDE4D and PPARG) mutually targeted by asthma genes and DCT compounds and 155 docking connections associated with cellular pathways involved in the biological mechanisms of asthma. Conclusions DCT compounds directly target biological pathways connected with the pathogenesis of asthma including inflammatory and metabolic signaling pathways.
format: application/pdf
format: text/html
creator: Allison Clyne
creator: Liping Yang
creator: Ming Yang
creator: Brian May
creator: Angela Wei Hong Yang
subject: Computational Biology
subject: Allergy and Clinical Immunology
subject: Pharmacology
subject: Respiratory Medicine
description: doi:10.7717/peerj.8685
publisher: PeerJ Inc.
rights: © 2020 Clyne et al.
abstract: Background Ding Chuan Tang (DCT), a traditional Chinese herbal formula, has been consistently prescribed for the therapeutic management of wheezing and asthma-related indications since the Song Dynasty (960–1279 AD). This study aimed to identify molecular network pharmacology connections to understand the biological asthma-linked mechanisms of action of DCT and potentially identify novel avenues for asthma drug development. Methods Employing molecular docking (AutoDock Vina) and computational analysis (Cytoscape 3.6.0) strategies for DCT compounds permitted examination of docking connections for proteins that were targets of DCT compounds and asthma genes. These identified protein targets were further analyzed to establish and interpret network connections associated with asthma disease pathways. Results A total of 396 DCT compounds and 234 asthma genes were identified through database search. Computational molecular docking of DCT compounds identified five proteins (ESR1, KDR, LTA4H, PDE4D and PPARG) mutually targeted by asthma genes and DCT compounds and 155 docking connections associated with cellular pathways involved in the biological mechanisms of asthma. Conclusions DCT compounds directly target biological pathways connected with the pathogenesis of asthma including inflammatory and metabolic signaling pathways.
bibliographic citation: Clyne et al. (2020) Molecular docking and network connections of active compounds from the classical herbal formula Ding Chuan Tang. PeerJ 8:e8685 https://doi.org/10.7717/peerj.8685
date submitted: 2019-10-03
date accepted: 2020-02-04
issued: 2020-03-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clyne
  given name: Allison
author list: Agent
  family name: Yang
  given name: Liping
author list: Agent
  family name: Yang
  given name: Ming
author list: Agent
  family name: May
  given name: Brian
author list: Agent
  family name: Yang
  given name: Angela Wei Hong
doi: 10.7717/peerj.8685
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-05
copyright: © 2020 Clyne et al.
attribution name: Clyne et al.

Diversity of fall armyworm, Spodoptera frugiperda and their gut bacterial community in Kenya
type: item
type: AcademicArticle
description: Background The invasive fall armyworm, Spodoptera frugiperda (J.E. Smith) is a polyphagous pest that causes widespread damage particularly to maize and sorghum in Africa. The microbiome associated with S. frugiperda could play a role in the insects’ success and adaptability. However, bacterial communities in S. frugiperda remain poorly studied. Methods We investigated the composition, abundance and diversity of microbiomes associated with larval and adult specimens of S. frugiperda collected from four maize growing regions in Kenya through high throughput sequencing of the bacterial 16S rRNA gene. The population structure of S. frugiperda in Kenya was assessed through amplification of the mitochondrial cytochrome oxidase subunit I gene. Results We identified Proteobacteria and Firmicutes as the most dominant bacterial phyla and lesser proportions of Bacteroidetes and Actinobacteria. We also observed differences in bacterial microbiome diversity between larvae and adults that are a likely indication that some prominent larval bacterial groups are lost during metamorphosis. However, several bacterial groups were found in both adults and larvae suggesting that they are transmitted across developmental stages. Reads corresponding to several known entomopathogenic bacterial clades as well as the fungal entomopathogen, Metarhizium rileyi, were observed. Mitochondrial DNA haplotyping of the S. frugiperda population in Kenya indicated the presence of both “Rice” and “Corn” strains, with a higher prevalence of the “Rice” strain.
format: application/pdf
format: text/html
creator: Joseph Gichuhi
creator: Subramanian Sevgan
creator: Fathiya Khamis
creator: Johnnie Van den Berg
creator: Hannalene du Plessis
creator: Sunday Ekesi
creator: Jeremy K. Herren
subject: Agricultural Science
subject: Entomology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.8701
publisher: PeerJ Inc.
rights: © 2020 Gichuhi et al.
abstract: Background The invasive fall armyworm, Spodoptera frugiperda (J.E. Smith) is a polyphagous pest that causes widespread damage particularly to maize and sorghum in Africa. The microbiome associated with S. frugiperda could play a role in the insects’ success and adaptability. However, bacterial communities in S. frugiperda remain poorly studied. Methods We investigated the composition, abundance and diversity of microbiomes associated with larval and adult specimens of S. frugiperda collected from four maize growing regions in Kenya through high throughput sequencing of the bacterial 16S rRNA gene. The population structure of S. frugiperda in Kenya was assessed through amplification of the mitochondrial cytochrome oxidase subunit I gene. Results We identified Proteobacteria and Firmicutes as the most dominant bacterial phyla and lesser proportions of Bacteroidetes and Actinobacteria. We also observed differences in bacterial microbiome diversity between larvae and adults that are a likely indication that some prominent larval bacterial groups are lost during metamorphosis. However, several bacterial groups were found in both adults and larvae suggesting that they are transmitted across developmental stages. Reads corresponding to several known entomopathogenic bacterial clades as well as the fungal entomopathogen, Metarhizium rileyi, were observed. Mitochondrial DNA haplotyping of the S. frugiperda population in Kenya indicated the presence of both “Rice” and “Corn” strains, with a higher prevalence of the “Rice” strain.
bibliographic citation: Gichuhi et al. (2020) Diversity of fall armyworm, Spodoptera frugiperda and their gut bacterial community in Kenya. PeerJ 8:e8701 https://doi.org/10.7717/peerj.8701
date submitted: 2019-10-21
date accepted: 2020-02-06
issued: 2020-03-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gichuhi
  given name: Joseph
author list: Agent
  family name: Sevgan
  given name: Subramanian
author list: Agent
  family name: Khamis
  given name: Fathiya
author list: Agent
  family name: Van den Berg
  given name: Johnnie
author list: Agent
  family name: du Plessis
  given name: Hannalene
author list: Agent
  family name: Ekesi
  given name: Sunday
author list: Agent
  family name: Herren
  given name: Jeremy K.
doi: 10.7717/peerj.8701
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-05
copyright: © 2020 Gichuhi et al.
attribution name: Gichuhi et al.

Application of a high-quality, high-volume trap–neuter–return model of community cats in Seoul, Korea
type: item
type: AcademicArticle
description: Background This study was performed to determine the characteristics of community cats that were admitted to trap–neuter–return(TNR) programs and the feasibility of the high-quality, high-volume spay/neuter (HQHVSN) model in Seoul, Korea. Methods TNR programs were performed eight times from 2017 to 2018, and a total of 375 community cats from the pilot areas were admitted. The pilot areas were selected regions wherein caregivers voluntarily participated in our TNR program. Each cat was anesthetized, assessed for health status, sterilized, vaccinated against feline viral rhinotracheitis, calicivirus and panleukopenia (FVR-CP), and rabies, and treated with insecticide after surgery. The time from anesthesia to recovery was evaluated to verify the efficiency of surgical time of the program. The TNR program at a local animal hospital and the program in this study were compared to assess the veterinary treatment administered and the cost for each cat. Results A total of 375 cats were underwent TNR in this study, including 192 (51.2%) intact females, 180 (48%) intact males, and three (0.8%) sterilized cats. Following surgery, 372 cats (99.2%) were returned to their original locations. Three cats (0.8%) died postoperatively. On average, 21.9% of the cats were pregnant during the TNRs, and the highest percentage of cats (63.9%) were pregnant in March. All cats presented to the TNR program were considered healthy enough to be part of the program after examination. For neutering one animal at a time, similar to conventional TNR ($140), it took 53 ± 16 mins for females and 30 ± 9 mins for males from anesthesia to recovery. In contrast, the standardized procedure can neuter multiple cats simultaneously, similar to the conveyor system, at an estimated rate of 6.8 mins per cat ($45 per female cat, $30 per male cat). Conclusions The TNR strategy in Seoul should be implemented by establishing dedicated clinics to concentrate on HQHVSN surgeries of cats. Through this pilot study, we…
format: application/pdf
format: text/html
creator: Yoonju Cho
creator: Kyunghee Kim
creator: Min Su Kim
creator: Inhyung Lee
subject: Animal Behavior
subject: Veterinary Medicine
subject: Zoology
subject: Ethical Issues
description: doi:10.7717/peerj.8711
publisher: PeerJ Inc.
rights: © 2020 Cho et al.
abstract: Background This study was performed to determine the characteristics of community cats that were admitted to trap–neuter–return(TNR) programs and the feasibility of the high-quality, high-volume spay/neuter (HQHVSN) model in Seoul, Korea. Methods TNR programs were performed eight times from 2017 to 2018, and a total of 375 community cats from the pilot areas were admitted. The pilot areas were selected regions wherein caregivers voluntarily participated in our TNR program. Each cat was anesthetized, assessed for health status, sterilized, vaccinated against feline viral rhinotracheitis, calicivirus and panleukopenia (FVR-CP), and rabies, and treated with insecticide after surgery. The time from anesthesia to recovery was evaluated to verify the efficiency of surgical time of the program. The TNR program at a local animal hospital and the program in this study were compared to assess the veterinary treatment administered and the cost for each cat. Results A total of 375 cats were underwent TNR in this study, including 192 (51.2%) intact females, 180 (48%) intact males, and three (0.8%) sterilized cats. Following surgery, 372 cats (99.2%) were returned to their original locations. Three cats (0.8%) died postoperatively. On average, 21.9% of the cats were pregnant during the TNRs, and the highest percentage of cats (63.9%) were pregnant in March. All cats presented to the TNR program were considered healthy enough to be part of the program after examination. For neutering one animal at a time, similar to conventional TNR ($140), it took 53 ± 16 mins for females and 30 ± 9 mins for males from anesthesia to recovery. In contrast, the standardized procedure can neuter multiple cats simultaneously, similar to the conveyor system, at an estimated rate of 6.8 mins per cat ($45 per female cat, $30 per male cat). Conclusions The TNR strategy in Seoul should be implemented by establishing dedicated clinics to concentrate on HQHVSN surgeries of cats. Through this pilot study, we…
bibliographic citation: Cho et al. (2020) Application of a high-quality, high-volume trap–neuter–return model of community cats in Seoul, Korea. PeerJ 8:e8711 https://doi.org/10.7717/peerj.8711
date submitted: 2019-10-28
date accepted: 2020-02-10
issued: 2020-03-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cho
  given name: Yoonju
author list: Agent
  family name: Kim
  given name: Kyunghee
author list: Agent
  family name: Kim
  given name: Min Su
author list: Agent
  family name: Lee
  given name: Inhyung
doi: 10.7717/peerj.8711
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-05
copyright: ©2020 Cho et al.
attribution name: Cho et al.

Congenital feeding response to a novel prey in a Mexican gartersnake
type: item
type: AcademicArticle
description: In this study, we explored chemosensory, ingestive and prey-catching responses of neonate Mexican Black-bellied Gartersnakes (Thamnophis melanogaster) to crayfish (Cambarellus montezumae). By comparing snakes from a recently discovered crayfish-eating population and a typical non-crayfish-eating population, we asked which behavioral components change as a species enlarges its feeding niche. In the crayfish-eating population chemosensory responsiveness to crayfish was not enhanced but its heritability was higher. Neonates of both populations showed similar preference for freshly-molted versus unmolted crayfish, and whereas the tendency to ingest both crayfish stages remained stable between ages 15 and 90 days in the non-crayfish-eating population, in the crayfish-eating population it actually decreased. Techniques to catch and manipulate molted crayfish were similar in the two populations. We discuss the possibility that there is no increase in the behavioral response to eat crayfish by the neonates of the crayfish-eating populations, possibly due to the absence of ecological and spatial isolation between the two T. melanogaster populations. The crayfish ingestion in some population of T. melanogaster can be explained by environmental differences between populations, or by recent origin of crayfish ingestion in T. melanogaster.
format: application/pdf
format: text/html
creator: Javier Manjarrez
creator: Constantino Macías Garcia
creator: Hugh Drummond
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.8718
publisher: PeerJ Inc.
rights: © 2020 Manjarrez et al.
abstract: In this study, we explored chemosensory, ingestive and prey-catching responses of neonate Mexican Black-bellied Gartersnakes (Thamnophis melanogaster) to crayfish (Cambarellus montezumae). By comparing snakes from a recently discovered crayfish-eating population and a typical non-crayfish-eating population, we asked which behavioral components change as a species enlarges its feeding niche. In the crayfish-eating population chemosensory responsiveness to crayfish was not enhanced but its heritability was higher. Neonates of both populations showed similar preference for freshly-molted versus unmolted crayfish, and whereas the tendency to ingest both crayfish stages remained stable between ages 15 and 90 days in the non-crayfish-eating population, in the crayfish-eating population it actually decreased. Techniques to catch and manipulate molted crayfish were similar in the two populations. We discuss the possibility that there is no increase in the behavioral response to eat crayfish by the neonates of the crayfish-eating populations, possibly due to the absence of ecological and spatial isolation between the two T. melanogaster populations. The crayfish ingestion in some population of T. melanogaster can be explained by environmental differences between populations, or by recent origin of crayfish ingestion in T. melanogaster.
bibliographic citation: Manjarrez et al. (2020) Congenital feeding response to a novel prey in a Mexican gartersnake. PeerJ 8:e8718 https://doi.org/10.7717/peerj.8718
date submitted: 2019-07-01
date accepted: 2020-02-10
issued: 2020-03-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manjarrez
  given name: Javier
author list: Agent
  family name: Macías Garcia
  given name: Constantino
author list: Agent
  family name: Drummond
  given name: Hugh
doi: 10.7717/peerj.8718
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-05
copyright: ©2020 Manjarrez et al.
attribution name: Manjarrez et al.

Genome-wide investigation of WRKY transcription factors in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating growth and development
type: item
type: AcademicArticle
description: Background The WRKY gene family plays important roles in plant biological functions and has been identified in many plant species. With the publication of the Tartary buckwheat genome, the evolutionary characteristics of the WRKY gene family can be systematically explored and the functions of Fagopyrum tataricum WRKY (FtWRKY) genes in the growth and development of this plant also can be predicted. Methods In this study, the FtWRKY genes were identified by the BLASTP method, and HMMER, SMART, Pfam and InterPro were used to determine whether the FtWRKY genes contained conserved domains. The phylogenetic trees including FtWRKY and WRKY genes in other plants were constructed by the neighbor-joining (NJ) and maximum likelihood (ML) methods. The intron and exon structures of the FtWRKY genes were analyzed by the gene structure display server, and the motif compositions were analyzed by MEME. Chromosome location information of FtWRKY genes was obtained with gff files and sequencing files, and visualized by Circos, and the collinear relationship was analyzed by Dual synteny plotter software. The expression levels of 26 FtWRKY genes from different groups in roots, leaves, flowers, stems and fruits at the green fruit, discoloration and initial maturity stage were measured through quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Results A total of 76 FtWRKY genes identified from the Tartary buckwheat genome were divided into three groups. FtWRKY genes in the same group had similar gene structures and motif compositions. Despite the lack of tandem-duplicated gene pairs, there were 23 pairs of segmental-duplicated gene pairs. The synteny gene pairs of FtWRKY genes and Glycine max WRKY genes were the most. FtWRKY42 was highly expressed in roots and may perform similar functions as its homologous gene AtWRKY75, playing a role in lateral root and hairy root formation. FtWRKY9, FtWRKY42 and FtWRKY60 were highly expressed in fruits and may play an important role i…
format: application/pdf
format: text/html
creator: Wenjun Sun
creator: Zhaotang Ma
creator: Hui Chen
creator: Moyang Liu
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.8727
publisher: PeerJ Inc.
rights: © 2020 Sun et al.
abstract: Background The WRKY gene family plays important roles in plant biological functions and has been identified in many plant species. With the publication of the Tartary buckwheat genome, the evolutionary characteristics of the WRKY gene family can be systematically explored and the functions of Fagopyrum tataricum WRKY (FtWRKY) genes in the growth and development of this plant also can be predicted. Methods In this study, the FtWRKY genes were identified by the BLASTP method, and HMMER, SMART, Pfam and InterPro were used to determine whether the FtWRKY genes contained conserved domains. The phylogenetic trees including FtWRKY and WRKY genes in other plants were constructed by the neighbor-joining (NJ) and maximum likelihood (ML) methods. The intron and exon structures of the FtWRKY genes were analyzed by the gene structure display server, and the motif compositions were analyzed by MEME. Chromosome location information of FtWRKY genes was obtained with gff files and sequencing files, and visualized by Circos, and the collinear relationship was analyzed by Dual synteny plotter software. The expression levels of 26 FtWRKY genes from different groups in roots, leaves, flowers, stems and fruits at the green fruit, discoloration and initial maturity stage were measured through quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Results A total of 76 FtWRKY genes identified from the Tartary buckwheat genome were divided into three groups. FtWRKY genes in the same group had similar gene structures and motif compositions. Despite the lack of tandem-duplicated gene pairs, there were 23 pairs of segmental-duplicated gene pairs. The synteny gene pairs of FtWRKY genes and Glycine max WRKY genes were the most. FtWRKY42 was highly expressed in roots and may perform similar functions as its homologous gene AtWRKY75, playing a role in lateral root and hairy root formation. FtWRKY9, FtWRKY42 and FtWRKY60 were highly expressed in fruits and may play an important role i…
bibliographic citation: Sun et al. (2020) Genome-wide investigation of WRKY transcription factors in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating growth and development. PeerJ 8:e8727 https://doi.org/10.7717/peerj.8727
date submitted: 2019-08-07
date accepted: 2020-02-10
issued: 2020-03-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Wenjun
author list: Agent
  family name: Ma
  given name: Zhaotang
author list: Agent
  family name: Chen
  given name: Hui
author list: Agent
  family name: Liu
  given name: Moyang
doi: 10.7717/peerj.8727
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-05
copyright: ©2020 Sun et al.
attribution name: Sun et al.

Common and specific gene signatures among three different endometriosis subtypes
type: item
type: AcademicArticle
description: Aims To identify the common and specific molecular mechanisms of three well-defined subtypes of endometriosis (EMs): ovarian endometriosis (OE), peritoneal endometriosis (PE), and deep infiltrating endometriosis (DIE). Methods Four microarray datasets: GSE7305 and GSE7307 for OE, E-MTAB-694 for PE, and GSE25628 for DIE were downloaded from public databases and conducted to compare ectopic lesions (EC) with eutopic endometrium (EU) from EMs patients. Differentially expressed genes (DEGs) identified by limma package were divided into two parts: common DEGs among three subtypes and specific DEGs in each subtype, both of which were subsequently performed with the Kyoto Encyclopedia of Genes (KEGG) pathway enrichment analysis. The protein-protein interaction (PPI) network was constructed by common DEGs and five hub genes were screened out from the PPI network. Besides, these five hub genes together with selected interested pathway-related genes were further validated in an independent OE RNA-sequencing dataset GSE105764. Results A total of 54 EC samples from three EMs subtypes (OE, PE, DIE) and 58 EU samples were analyzed, from which we obtained 148 common DEGs among three subtypes, and 729 specific DEGs in OE, 777 specific DEGs in PE and 36 specific DEGs in DIE. The most enriched pathway of 148 shared DEGs was arachidonic acid (AA) metabolism, in which most genes were up-regulated in EC, indicating inflammation was the most common pathogenesis of three subtypes. Besides, five hub genes AURKB, RRM2, DTL, CCNB1, CCNB2 identified from the PPI network constructed by 148 shared DEGs were all associated with cell cycle and mitosis, and down-regulated in EC, suggesting a slow and controlled proliferation in ectopic lesions. The KEGG pathway analysis of specific DEGs in each subtype revealed that abnormal ovarian steroidogenesis was a prominent feature in OE; OE and DIE seems to be at more risk of malignant development since both of their specific DEGs were enriched in the path…
format: application/pdf
format: text/html
creator: Li Jiang
creator: Mengmeng Zhang
creator: Sixue Wang
creator: Yuanyuan Han
creator: Xiaoling Fang
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.8730
publisher: PeerJ Inc.
rights: © 2020 Jiang et al.
abstract: Aims To identify the common and specific molecular mechanisms of three well-defined subtypes of endometriosis (EMs): ovarian endometriosis (OE), peritoneal endometriosis (PE), and deep infiltrating endometriosis (DIE). Methods Four microarray datasets: GSE7305 and GSE7307 for OE, E-MTAB-694 for PE, and GSE25628 for DIE were downloaded from public databases and conducted to compare ectopic lesions (EC) with eutopic endometrium (EU) from EMs patients. Differentially expressed genes (DEGs) identified by limma package were divided into two parts: common DEGs among three subtypes and specific DEGs in each subtype, both of which were subsequently performed with the Kyoto Encyclopedia of Genes (KEGG) pathway enrichment analysis. The protein-protein interaction (PPI) network was constructed by common DEGs and five hub genes were screened out from the PPI network. Besides, these five hub genes together with selected interested pathway-related genes were further validated in an independent OE RNA-sequencing dataset GSE105764. Results A total of 54 EC samples from three EMs subtypes (OE, PE, DIE) and 58 EU samples were analyzed, from which we obtained 148 common DEGs among three subtypes, and 729 specific DEGs in OE, 777 specific DEGs in PE and 36 specific DEGs in DIE. The most enriched pathway of 148 shared DEGs was arachidonic acid (AA) metabolism, in which most genes were up-regulated in EC, indicating inflammation was the most common pathogenesis of three subtypes. Besides, five hub genes AURKB, RRM2, DTL, CCNB1, CCNB2 identified from the PPI network constructed by 148 shared DEGs were all associated with cell cycle and mitosis, and down-regulated in EC, suggesting a slow and controlled proliferation in ectopic lesions. The KEGG pathway analysis of specific DEGs in each subtype revealed that abnormal ovarian steroidogenesis was a prominent feature in OE; OE and DIE seems to be at more risk of malignant development since both of their specific DEGs were enriched in the path…
bibliographic citation: Jiang et al. (2020) Common and specific gene signatures among three different endometriosis subtypes. PeerJ 8:e8730 https://doi.org/10.7717/peerj.8730
date submitted: 2019-08-07
date accepted: 2020-02-11
issued: 2020-03-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Li
author list: Agent
  family name: Zhang
  given name: Mengmeng
author list: Agent
  family name: Wang
  given name: Sixue
author list: Agent
  family name: Han
  given name: Yuanyuan
author list: Agent
  family name: Fang
  given name: Xiaoling
doi: 10.7717/peerj.8730
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-05
copyright: ©2020 Jiang et al.
attribution name: Jiang et al.

Characterisation of GLUT4 trafficking in HeLa cells: comparable kinetics and orthologous trafficking mechanisms to 3T3-L1 adipocytes
type: item
type: AcademicArticle
description: Insulin-stimulated glucose transport is a characteristic property of adipocytes and muscle cells and involves the regulated delivery of glucose transporter (GLUT4)-containing vesicles from intracellular stores to the cell surface. Fusion of these vesicles results in increased numbers of GLUT4 molecules at the cell surface. In an attempt to overcome some of the limitations associated with both primary and cultured adipocytes, we expressed an epitope- and GFP-tagged version of GLUT4 (HA–GLUT4–GFP) in HeLa cells. Here we report the characterisation of this system compared to 3T3-L1 adipocytes. We show that insulin promotes translocation of HA–GLUT4–GFP to the surface of both cell types with similar kinetics using orthologous trafficking machinery. While the magnitude of the insulin-stimulated translocation of GLUT4 is smaller than mouse 3T3-L1 adipocytes, HeLa cells offer a useful, experimentally tractable, human model system. Here, we exemplify their utility through a small-scale siRNA screen to identify GOSR1 and YKT6 as potential novel regulators of GLUT4 trafficking in human cells.
format: application/pdf
format: text/html
creator: Silke Morris
creator: Niall D. Geoghegan
creator: Jessica B.A. Sadler
creator: Anna M. Koester
creator: Hannah L. Black
creator: Marco Laub
creator: Lucy Miller
creator: Linda Heffernan
creator: Jeremy C. Simpson
creator: Cynthia C. Mastick
creator: Jon Cooper
creator: Nikolaj Gadegaard
creator: Nia J. Bryant
creator: Gwyn W. Gould
subject: Biochemistry
subject: Cell Biology
description: doi:10.7717/peerj.8751
publisher: PeerJ Inc.
rights: © 2020 Morris et al.
abstract: Insulin-stimulated glucose transport is a characteristic property of adipocytes and muscle cells and involves the regulated delivery of glucose transporter (GLUT4)-containing vesicles from intracellular stores to the cell surface. Fusion of these vesicles results in increased numbers of GLUT4 molecules at the cell surface. In an attempt to overcome some of the limitations associated with both primary and cultured adipocytes, we expressed an epitope- and GFP-tagged version of GLUT4 (HA–GLUT4–GFP) in HeLa cells. Here we report the characterisation of this system compared to 3T3-L1 adipocytes. We show that insulin promotes translocation of HA–GLUT4–GFP to the surface of both cell types with similar kinetics using orthologous trafficking machinery. While the magnitude of the insulin-stimulated translocation of GLUT4 is smaller than mouse 3T3-L1 adipocytes, HeLa cells offer a useful, experimentally tractable, human model system. Here, we exemplify their utility through a small-scale siRNA screen to identify GOSR1 and YKT6 as potential novel regulators of GLUT4 trafficking in human cells.
bibliographic citation: Morris et al. (2020) Characterisation of GLUT4 trafficking in HeLa cells: comparable kinetics and orthologous trafficking mechanisms to 3T3-L1 adipocytes. PeerJ 8:e8751 https://doi.org/10.7717/peerj.8751
date submitted: 2019-12-16
date accepted: 2020-02-14
issued: 2020-03-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morris
  given name: Silke
author list: Agent
  family name: Geoghegan
  given name: Niall D.
author list: Agent
  family name: Sadler
  given name: Jessica B.A.
author list: Agent
  family name: Koester
  given name: Anna M.
author list: Agent
  family name: Black
  given name: Hannah L.
author list: Agent
  family name: Laub
  given name: Marco
author list: Agent
  family name: Miller
  given name: Lucy
author list: Agent
  family name: Heffernan
  given name: Linda
author list: Agent
  family name: Simpson
  given name: Jeremy C.
author list: Agent
  family name: Mastick
  given name: Cynthia C.
author list: Agent
  family name: Cooper
  given name: Jon
author list: Agent
  family name: Gadegaard
  given name: Nikolaj
author list: Agent
  family name: Bryant
  given name: Nia J.
author list: Agent
  family name: Gould
  given name: Gwyn W.
doi: 10.7717/peerj.8751
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-03-05
copyright: © 2020 Morris et al.
attribution name: Morris et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359